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Structural studies on a non-toxic homologue of type II RIPs from Momordica charantia (bitter gourd) in complex with galactose.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Z8S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 298 0.1M HEPES, 20% w/v PEG 10000, glycerol
Crystal Properties Matthews coefficient Solvent content 3.64 66.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.3 α = 90 b = 137.07 β = 90 c = 44.84 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2012-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.533 142.3 99 0.143 11.7 6 29954
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.53 2.67 93.4 0.8 2.4 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4Z8S 2.54 68.54 26773 1434 94 0.183 0.18 0.1899 0.231 0.233 RANDOM 24.24
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.26 0.07 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.907 r_dihedral_angle_4_deg 18.772 r_dihedral_angle_3_deg 13.613 r_dihedral_angle_1_deg 7.333 r_long_range_B_refined 5.248 r_long_range_B_other 5.191 r_scangle_other 3.077 r_mcangle_it 2.581 r_mcangle_other 2.58 r_scbond_it 1.921
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.907 r_dihedral_angle_4_deg 18.772 r_dihedral_angle_3_deg 13.613 r_dihedral_angle_1_deg 7.333 r_long_range_B_refined 5.248 r_long_range_B_other 5.191 r_scangle_other 3.077 r_mcangle_it 2.581 r_mcangle_other 2.58 r_scbond_it 1.921 r_scbond_other 1.921 r_angle_refined_deg 1.666 r_mcbond_it 1.536 r_mcbond_other 1.536 r_angle_other_deg 1.224 r_chiral_restr 0.152 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3960 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing MOSFLM data collection